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Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer

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Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer Hindawi BioMed Research International Volume 2020, Article ID 4712498, 11 pages https://doi.org/10.1155/2020/4712498 Research Article Characterization of Oral Microbiome and Exploration of Potential Biomarkers in Patients with Pancreatic Cancer Haiyang Sun,1 Xia Zhao,2 Yanxia Zhou,1 Jun Wang,1 Rui Ma,1 Xi Ren,1 Huaizhi Wang ,3 and Lingyun Zou 1 1Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, 518102 Shenzhen, China 2Bioinformatics Center, Department of Microbiology, Army Medical University, 400038 Chongqing, China 3Institute of Hepatopancreatobiliary Surgery, Chongqing General Hospital, University of Chinese Academy of Sciences, China Correspondence should be addressed to Huaizhi Wang; [email protected] and Lingyun Zou; [email protected] Received 26 May 2020; Revised 8 September 2020; Accepted 29 September 2020; Published 2 November 2020 Academic Editor: Koichiro Wada Copyright © 2020 Haiyang Sun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pancreatic cancer (PC) is highly malignant and lacks an effective therapeutic schedule, hence that early diagnosis is of great importance to achieve a good prognosis. Oral bacteria have been proved to be associated with pancreatic cancer, but the specific mechanism has not been comprehensively illustrated. In our study, thirty-seven saliva samples in total were collected with ten from PC patients, seventeen from benign pancreatic disease (BPD) patients, and ten from healthy controls (HC). The oral bacterial community of HC, PC, and BPD groups was profiled by 16S rDNA high-throughput sequencing and bioinformatic methods. As shown by Simpson, Inverse Simpson, Shannon and Heip, oral microbiome diversity of HC, BPD and PC groups is in increasing order with the BPD and PC groups significantly higher than the HC group. Principal coordinate analysis (PCoA) suggested that grouping by PC, BPD and HC was statistically significant. The linear discriminant analysis effect size (LEfSe) identified high concentrations of Fusobacterium periodonticum and low concentrations of Neisseria mucosa as specific risk factors for PC. Furthermore, predicted functions showed changes such as RNA processing and modification as well as the pathway of NOD-like receptor signaling occurred in both PC and HC groups. Conclusively, our findings have confirmed the destruction of oral bacterial community balance among patients with PC and BPD and indicated the potential of Fusobacterium periodonticum and Neisseria mucosa as diagnostic biomarkers of PC. 1. Introduction the regions with the highest microbiome density and the larg- est number of species in the body [10]. Many studies have Pancreatic cancer (PC) is a common malignant tumor, leading demonstrated that oral bacteria play an important role in the to around 432,242 deaths worldwide in 2018 [1]. Patients in the development of cancer, especially the tumors of oral and gas- early stage of PC have few symptoms, and the disease is com- trointestinal tract [11]. For example, Fusobacterium nuclea- monly diagnosed during intermediate and advanced stages tum and Porphyromonas gingivalis have been frequently for which there is no effective clinical treatment [2]. The five- researched and discussed [12–14]. The oral microbes can year relative survival rate of PC patients was around 9% [3]. communicate with other tissues of the digestive system Therefore, looking for new potential biomarkers will benefit through blood circulation, lymphokines, or biliary conduction PC patient’s early diagnosis greatly. CA19.9 (carbohydrate [15], and oral bacteria were usually associated with cancer of antigen 19.9) was released into blood by PC cells and widely the entire digestive system [16]. Previous 16S sequencing stud- used in clinical diagnosis [4, 5]. However, the testing result ies revealed the crucial role of oral bacteria in the development based on CA19.9, as well as other serological markers such as of pancreatic cancer, and several potential bacterial bio- CEA (carcinoembryonic antigen) are not so reliable [6–8]. markers were identified including Aggregatibacter actinomyce- Lots of diseases were related to the imbalance in the temcomitans, Neisseria elongata, Porphyromonas gingivalis, body’s microbiome [4, 9]. Actually, the oral cavity is one of and Streptococcus mitis [17–19]. It can thus be seen that the 2 BioMed Research International ° community composition of oral microbes provided clues for at -80 C within 1 hour. Samples mixed with blood are early diagnosis, monitoring, prevention, and treatment of PC. not retained. The serological markers are generally secreted into pan- creatic juice or blood via pancreatic epithelial tissue cells, 2.2. DNA Isolation, PCR, and Sequencing. The bacterial DNA hence sampling is inconvenient. However, sampling saliva was extracted from the salivary samples using the FastDNA® and test of it are relatively easy. Although several oral bacteria SPIN Kit for Soil (Majorbio, Shanghai, China) following the are found to be related with PC, the association between oral manufacturer’s protocol, and DNAs were quantified via bacteria and PC as well as BPD and the pathogenic mecha- NanoDrop 2000. The V3–V4 region of the bacterial 16S nism were not explored sufficiently [12, 14]. Under such cir- ribosomal RNA (rRNA) gene, which is generally considered cumstances, we carried out this research to discover new the standard target, was PCR-amplified using universal available salivary biomarkers of PC, and to comprehensively primers 338F 5′-ACTCCTACGGGAGGCAGCAG-3′ and explain the potential mechanism of oral microbes in the 806R 5′-GGACTACHVGGGTWTCTAAT-3′. Meanwhile, pathogenesis of PC. Thirty-seven saliva samples were col- an eight-base sequence served as the barcode was added, lected from ten PC patients, seventeen BPD patients, and which was unique to each sample. PCR reactions (20 μL) ten HC subjects. Based on 16S rDNA sequencing results, contained 4 μL of 5x FastPfu Buffer, 2 μL of 2.5 mM dNTPs, we compared the microbial community among the three 0.8 μL of each primer (5 μM), 0.4 μL of TransStart FastPfu groups and demonstrated that microbiome diversity in both DNA Polymerase, 0.2 μL BSA, 10 ng template DNA, and the BPD and PC groups was greatly higher than that in the ddH O. Thermal cycling consisted of the initial denaturation 2° ° ° HC group. LEfSe outputs disclosed that Fusobacterium peri- at 95 C for 2 min, followed by 25 cycles at 95 C for 30 s, 55 C ° ° odonticum and Neisseria mucosa may be the potential bio- for 30 s, 72 C for 45 s and a final extension at 72 C for 10 min. markers of PC. Furtherly, the predicted bacterial gene The construction of high-throughput sequencing libraries functions as well as the enriched pathways showed the signif- and pair-end sequencing was performed using the Illumina icant variance between PC and HC groups concerning RNA MiSeq platform according to the manufacturer’s recommen- processing and modification and enriched pathways such as dations. Finally, all the raw reads were deposited into the the pathway of NOD-like receptor signaling. Our findings NCBI Sequence Read Archive (SRA) database (Bioproject found the association between oral bacteria and PC, and pos- accession Number: SRP237984). sible applications of oral bacteria in diagnostic and treatment strategies for PC. 2.3. Bioinformatic and Statistical Analysis. Firstly, after the raw DNA fragments were generated, we merged the paired- 2. Materials and Methods end reads into a single sequence by means of using FLASH software v.1.2.10 (Fast Length Adjustment of SHort reads) 2.1. Subjects and Sample Collection. A total of ten PC patients, [20]. Then, 16S rRNA OTUs (operational taxonomic units) seventeen BPD patients and ten HC subjects were enrolled in were selected from the combined reads via QIIME toolkit this study. Exclusion criteria included antibiotic treatment v.1.9.1 (Quantitative Insights into Microbial Ecology) [21]. within 8 weeks, oral disease, digestive disease, genetic disease, Note that sequences with 97% identity were assigned to the other cancers and immune system diseases at the time of same OTU and the one with the highest frequencies was sample collection. Both PC and BPD groups were diagnosed selected as the representative sequence. Thirdly, we used by endoscopic ultrasonography and histopathologic the RDP classifier v.2.2 (The Ribosomal Database Project) examination at the First Hospital Affiliated to Army Medical to annotate taxonomic information for each representative University, China. It should be noted that the BPD group sequence [22]. Before performing the subsequent analysis, includes pancreatitis, chronic pancreatitis, and benign pan- we used USEARCH 11 to randomly select an equal number creatic tumors. This study was approved by the Ethics Board of OTU sequences for all samples according to the minimum at the Army Medical University and performed in accor- number of OTU sequences in samples. And next, based on dance with the Helsinki Declaration and Rules of Good the subordinate OTUs of different research groups, the corre- Clinical Practice. Written informed consent upon enrollment sponding alpha diversity was calculated on the indexes that as well as questionnaires addressing past medical history and include Simpson, Heip and Shannon. Note that Simpson lifestyles was obtained from all the volunteers. employed here shows the negative correlation with bacterial
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